kneaddata v0.12.0
I have some files with names sample1_R1.fastq.gz and sample1_R2.fastq.gz. When running kneaddata with the option --bypass-trim the next error occurs:
Decompressing gzipped file ...
Decompressing gzipped file ...
Reformatting file sequence identifiers ...
Reformatting file sequence identifiers ...
Initial number of reads ( /A2/danielpalma/projects/smk-metagenome/resources/test/fastq/knead/kneaddata_output/reformatted_identifiers4vawf0jt_decompressed_9r8knfr8_sample1_R1 ): 191296.0
Initial number of reads ( /A2/danielpalma/projects/smk-metagenome/resources/test/fastq/knead/kneaddata_output/reformatted_identifiersef0c7wrw_decompressed_hel63yku_sample1_R2 ): 191296.0
Running fastqc ...
Bypass trimming
Total reads after trimming ( /A2/danielpalma/projects/smk-metagenome/resources/test/fastq/knead/kneaddata_output/reformatted_identifiers4vawf0jt_decompressed_9r8knfr8_sample1_R1 ): 191296.0
Total reads after trimming ( /A2/danielpalma/projects/smk-metagenome/resources/test/fastq/knead/kneaddata_output/reformatted_identifiersef0c7wrw_decompressed_hel63yku_sample1_R2 ): 191296.0
ERROR: Unable to write file: /A2/danielpalma/projects/smk-metagenome/resources/test/fastq/knead/kneaddata_output/reformatted_identifiers4vawf0jt_decompressed_9r8knfr8_sample1_R1
But if I rename the files to sample1.1.fastq.gz and sample1.2.fastq.gz all its ok. I can work with that but it is a little inconvenient